Here's the call in plain terms. San Miguel gives you the best value and the most to do on foot. You walk to dinner, hop between bars, book a dive with the shop down the street, and never touch a rental car. The cost is the beaches: the in-town water is rocky, so swimming means a beach club or a boat.
The hotel zones flip all of that. You get calm beaches, a pool, and the resort switch-off some trips are built around. What you give up is reach. Dinner near your hotel is limited, and getting into town is a taxi each way or a rental car, and those fares stack up over a week, so count them in before you book.
There's no single right answer, just the right one for your trip. Want nightlife, food variety, and value with no car? Stay in town. Want quiet days by the water and you're fine paying to get around? Pick a hotel zone, north for the calm beaches, south to wake up near the dive sites.
One week a year that trade-off stops being a trade-off. During Carnaval, the waterfront avenue closes to traffic for the parades and taxis will not cross it, so a hotel zone room turns into a long ride to a drop off point and a worse one home at midnight with the whole island trying to do the same thing. That week, town wins outright.